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Comparing branches/development/src/brains/SimCreator.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1798 by gezelter, Thu Sep 13 14:10:11 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 55 | Line 56
56   #include "brains/SimCreator.hpp"
57   #include "brains/SimSnapshotManager.hpp"
58   #include "io/DumpReader.hpp"
59 < #include "UseTheForce/ForceFieldFactory.hpp"
59 > #include "brains/ForceField.hpp"
60   #include "utils/simError.h"
61   #include "utils/StringUtils.hpp"
62   #include "math/SeqRandNumGen.hpp"
# Line 75 | Line 76
76   #include "antlr/NoViableAltForCharException.hpp"
77   #include "antlr/NoViableAltException.hpp"
78  
79 + #include "types/DirectionalAdapter.hpp"
80 + #include "types/MultipoleAdapter.hpp"
81 + #include "types/EAMAdapter.hpp"
82 + #include "types/SuttonChenAdapter.hpp"
83 + #include "types/PolarizableAdapter.hpp"
84 + #include "types/FixedChargeAdapter.hpp"
85 + #include "types/FluctuatingChargeAdapter.hpp"
86 +
87   #ifdef IS_MPI
88 + #include "mpi.h"
89   #include "math/ParallelRandNumGen.hpp"
90   #endif
91  
92   namespace OpenMD {
93    
94 <  Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
94 >  Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
95      Globals* simParams = NULL;
96      try {
97  
# Line 92 | Line 102 | namespace OpenMD {
102        const int masterNode = 0;
103        int commStatus;
104        if (worldRank == masterNode) {
105 < #endif
106 <                
105 >        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
106 > #endif                
107          SimplePreprocessor preprocessor;
108          preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
109                  
# Line 106 | Line 116 | namespace OpenMD {
116              
117                  
118        } else {
119 +
120 +        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
121 +
122          //get stream size
123          commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
124  
# Line 229 | Line 242 | namespace OpenMD {
242        simError();
243      }
244  
245 +    simParams->setMDfileVersion(mdFileVersion);
246      return simParams;
247    }
248    
249    SimInfo*  SimCreator::createSim(const std::string & mdFileName,
250                                    bool loadInitCoords) {
251 <
251 >    
252      const int bufferSize = 65535;
253      char buffer[bufferSize];
254      int lineNo = 0;
# Line 242 | Line 256 | namespace OpenMD {
256      int metaDataBlockStart = -1;
257      int metaDataBlockEnd = -1;
258      int i;
259 <    int mdOffset;
259 >    streamoff mdOffset;
260 >    int mdFileVersion;
261  
262 +
263   #ifdef IS_MPI            
264      const int masterNode = 0;
265      if (worldRank == masterNode) {
266   #endif
267  
268 <      std::ifstream mdFile_(mdFileName.c_str());
268 >      std::ifstream mdFile_;
269 >      mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
270        
271        if (mdFile_.fail()) {
272          sprintf(painCave.errMsg,
# Line 276 | Line 293 | namespace OpenMD {
293          painCave.isFatal = 1;
294          simError();
295        }
296 +      
297 +      // found the correct opening string, now try to get the file
298 +      // format version number.
299 +
300 +      StringTokenizer tokenizer(line, "=<> \t\n\r");
301 +      std::string fileType = tokenizer.nextToken();
302 +      toUpper(fileType);
303 +
304 +      mdFileVersion = 0;
305  
306 +      if (fileType == "OPENMD") {
307 +        while (tokenizer.hasMoreTokens()) {
308 +          std::string token(tokenizer.nextToken());
309 +          toUpper(token);
310 +          if (token == "VERSION") {
311 +            mdFileVersion = tokenizer.nextTokenAsInt();
312 +            break;
313 +          }
314 +        }
315 +      }
316 +            
317        //scan through the input stream and find MetaData tag        
318        while(mdFile_.getline(buffer, bufferSize)) {
319          ++lineNo;
# Line 332 | Line 369 | namespace OpenMD {
369      std::stringstream rawMetaDataStream(mdRawData);
370  
371      //parse meta-data file
372 <    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1);
372 >    Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
373 >                                   metaDataBlockStart + 1);
374      
375      //create the force field
376 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField());
376 >    ForceField * ff = new ForceField(simParams->getForceField());
377  
378      if (ff == NULL) {
379        sprintf(painCave.errMsg,
# Line 369 | Line 407 | namespace OpenMD {
407      }
408      
409      ff->parse(forcefieldFileName);
372 –    ff->setFortranForceOptions();
410      //create SimInfo
411      SimInfo * info = new SimInfo(ff, simParams);
412  
# Line 387 | Line 424 | namespace OpenMD {
424      //create the molecules
425      createMolecules(info);
426      
427 <    
427 >    //find the storage layout
428 >
429 >    int storageLayout = computeStorageLayout(info);
430 >
431      //allocate memory for DataStorage(circular reference, need to
432      //break it)
433 <    info->setSnapshotManager(new SimSnapshotManager(info));
433 >    info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
434      
435      //set the global index of atoms, rigidbodies and cutoffgroups
436      //(only need to be set once, the global index will never change
# Line 413 | Line 453 | namespace OpenMD {
453      
454      if (loadInitCoords)
455        loadCoordinates(info, mdFileName);    
416 –    
456      return info;
457    }
458    
# Line 468 | Line 507 | namespace OpenMD {
507      int nGlobalMols = info->getNGlobalMolecules();
508      std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
509      
510 <    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
510 >    nProcessors = MPI::COMM_WORLD.Get_size();
511      
512      if (nProcessors > nGlobalMols) {
513        sprintf(painCave.errMsg,
# Line 583 | Line 622 | namespace OpenMD {
622        delete myRandom;
623        
624        // Spray out this nonsense to all other processors:
625 <      
587 <      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
625 >      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
626      } else {
627        
628        // Listen to your marching orders from processor 0:
629 <      
592 <      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
629 >      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
630      }
631      
632      info->setMolToProcMap(molToProcMap);
# Line 612 | Line 649 | namespace OpenMD {
649   #endif
650          
651          stampId = info->getMoleculeStampId(i);
652 <        Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
653 <                                                   stampId, i, info->getLocalIndexManager());
652 >        Molecule * mol = molCreator.createMolecule(info->getForceField(),
653 >                                                   info->getMoleculeStamp(stampId),
654 >                                                   stampId, i,
655 >                                                   info->getLocalIndexManager());
656          
657          info->addMolecule(mol);
658          
# Line 626 | Line 665 | namespace OpenMD {
665      } //end for(int i=0)  
666    }
667      
668 +  int SimCreator::computeStorageLayout(SimInfo* info) {
669 +
670 +    Globals* simParams = info->getSimParams();
671 +    int nRigidBodies = info->getNGlobalRigidBodies();
672 +    set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
673 +    set<AtomType*>::iterator i;
674 +    bool hasDirectionalAtoms = false;
675 +    bool hasFixedCharge = false;
676 +    bool hasDipoles = false;    
677 +    bool hasQuadrupoles = false;    
678 +    bool hasPolarizable = false;    
679 +    bool hasFluctuatingCharge = false;    
680 +    bool hasMetallic = false;
681 +    int storageLayout = 0;
682 +    storageLayout |= DataStorage::dslPosition;
683 +    storageLayout |= DataStorage::dslVelocity;
684 +    storageLayout |= DataStorage::dslForce;
685 +
686 +    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
687 +
688 +      DirectionalAdapter da = DirectionalAdapter( (*i) );
689 +      MultipoleAdapter ma = MultipoleAdapter( (*i) );
690 +      EAMAdapter ea = EAMAdapter( (*i) );
691 +      SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
692 +      PolarizableAdapter pa = PolarizableAdapter( (*i) );
693 +      FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
694 +      FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
695 +
696 +      if (da.isDirectional()){
697 +        hasDirectionalAtoms = true;
698 +      }
699 +      if (ma.isDipole()){
700 +        hasDipoles = true;
701 +      }
702 +      if (ma.isQuadrupole()){
703 +        hasQuadrupoles = true;
704 +      }
705 +      if (ea.isEAM() || sca.isSuttonChen()){
706 +        hasMetallic = true;
707 +      }
708 +      if ( fca.isFixedCharge() ){
709 +        hasFixedCharge = true;
710 +      }
711 +      if ( fqa.isFluctuatingCharge() ){
712 +        hasFluctuatingCharge = true;
713 +      }
714 +      if ( pa.isPolarizable() ){
715 +        hasPolarizable = true;
716 +      }
717 +    }
718 +    
719 +    if (nRigidBodies > 0 || hasDirectionalAtoms) {
720 +      storageLayout |= DataStorage::dslAmat;
721 +      if(storageLayout & DataStorage::dslVelocity) {
722 +        storageLayout |= DataStorage::dslAngularMomentum;
723 +      }
724 +      if (storageLayout & DataStorage::dslForce) {
725 +        storageLayout |= DataStorage::dslTorque;
726 +      }
727 +    }
728 +    if (hasDipoles) {
729 +      storageLayout |= DataStorage::dslDipole;
730 +    }
731 +    if (hasQuadrupoles) {
732 +      storageLayout |= DataStorage::dslQuadrupole;
733 +    }
734 +    if (hasFixedCharge || hasFluctuatingCharge) {
735 +      storageLayout |= DataStorage::dslSkippedCharge;
736 +    }
737 +    if (hasMetallic) {
738 +      storageLayout |= DataStorage::dslDensity;
739 +      storageLayout |= DataStorage::dslFunctional;
740 +      storageLayout |= DataStorage::dslFunctionalDerivative;
741 +    }
742 +    if (hasPolarizable) {
743 +      storageLayout |= DataStorage::dslElectricField;
744 +    }
745 +    if (hasFluctuatingCharge){
746 +      storageLayout |= DataStorage::dslFlucQPosition;
747 +      if(storageLayout & DataStorage::dslVelocity) {
748 +        storageLayout |= DataStorage::dslFlucQVelocity;
749 +      }
750 +      if (storageLayout & DataStorage::dslForce) {
751 +        storageLayout |= DataStorage::dslFlucQForce;
752 +      }
753 +    }
754 +    
755 +    // if the user has asked for them, make sure we've got the memory for the
756 +    // objects defined.
757 +
758 +    if (simParams->getOutputParticlePotential()) {
759 +      storageLayout |= DataStorage::dslParticlePot;
760 +    }
761 +
762 +    if (simParams->havePrintHeatFlux()) {
763 +      if (simParams->getPrintHeatFlux()) {
764 +        storageLayout |= DataStorage::dslParticlePot;
765 +      }
766 +    }
767 +
768 +    if (simParams->getOutputElectricField()) {
769 +      storageLayout |= DataStorage::dslElectricField;
770 +    }
771 +
772 +    if (simParams->getOutputFluctuatingCharges()) {
773 +      storageLayout |= DataStorage::dslFlucQPosition;
774 +      storageLayout |= DataStorage::dslFlucQVelocity;
775 +      storageLayout |= DataStorage::dslFlucQForce;
776 +    }
777 +
778 +    return storageLayout;
779 +  }
780 +
781    void SimCreator::setGlobalIndex(SimInfo *info) {
782      SimInfo::MoleculeIterator mi;
783      Molecule::AtomIterator ai;
# Line 640 | Line 792 | namespace OpenMD {
792      int beginRigidBodyIndex;
793      int beginCutoffGroupIndex;
794      int nGlobalAtoms = info->getNGlobalAtoms();
643 –
644 –    /**@todo fixme */
645 – #ifndef IS_MPI
795      
796      beginAtomIndex = 0;
648 –    beginRigidBodyIndex = 0;
649 –    beginCutoffGroupIndex = 0;
650 –    
651 – #else
652 –    
653 –    int nproc;
654 –    int myNode;
655 –    
656 –    myNode = worldRank;
657 –    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
658 –    
659 –    std::vector < int > tmpAtomsInProc(nproc, 0);
660 –    std::vector < int > tmpRigidBodiesInProc(nproc, 0);
661 –    std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
662 –    std::vector < int > NumAtomsInProc(nproc, 0);
663 –    std::vector < int > NumRigidBodiesInProc(nproc, 0);
664 –    std::vector < int > NumCutoffGroupsInProc(nproc, 0);
665 –    
666 –    tmpAtomsInProc[myNode] = info->getNAtoms();
667 –    tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
668 –    tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
669 –    
670 –    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
671 –    MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
672 –                  MPI_SUM, MPI_COMM_WORLD);
673 –    MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
674 –                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
675 –    MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
676 –                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
677 –    
678 –    beginAtomIndex = 0;
679 –    beginRigidBodyIndex = 0;
680 –    beginCutoffGroupIndex = 0;
681 –    
682 –    for(int i = 0; i < myNode; i++) {
683 –      beginAtomIndex += NumAtomsInProc[i];
684 –      beginRigidBodyIndex += NumRigidBodiesInProc[i];
685 –      beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
686 –    }
687 –    
688 – #endif
689 –    
797      //rigidbody's index begins right after atom's
798 <    beginRigidBodyIndex += info->getNGlobalAtoms();
799 <    
800 <    for(mol = info->beginMolecule(mi); mol != NULL;
801 <        mol = info->nextMolecule(mi)) {
798 >    beginRigidBodyIndex = info->getNGlobalAtoms();
799 >    beginCutoffGroupIndex = 0;
800 >
801 >    for(int i = 0; i < info->getNGlobalMolecules(); i++) {
802        
803 <      //local index(index in DataStorge) of atom is important
804 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
805 <        atom->setGlobalIndex(beginAtomIndex++);
803 > #ifdef IS_MPI      
804 >      if (info->getMolToProc(i) == worldRank) {
805 > #endif        
806 >        // stuff to do if I own this molecule
807 >        mol = info->getMoleculeByGlobalIndex(i);
808 >
809 >        //local index(index in DataStorge) of atom is important
810 >        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
811 >          atom->setGlobalIndex(beginAtomIndex++);
812 >        }
813 >        
814 >        for(rb = mol->beginRigidBody(ri); rb != NULL;
815 >            rb = mol->nextRigidBody(ri)) {
816 >          rb->setGlobalIndex(beginRigidBodyIndex++);
817 >        }
818 >        
819 >        //local index of cutoff group is trivial, it only depends on
820 >        //the order of travesing
821 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
822 >            cg = mol->nextCutoffGroup(ci)) {
823 >          cg->setGlobalIndex(beginCutoffGroupIndex++);
824 >        }        
825 >        
826 > #ifdef IS_MPI        
827 >      }  else {
828 >
829 >        // stuff to do if I don't own this molecule
830 >        
831 >        int stampId = info->getMoleculeStampId(i);
832 >        MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
833 >
834 >        beginAtomIndex += stamp->getNAtoms();
835 >        beginRigidBodyIndex += stamp->getNRigidBodies();
836 >        beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
837        }
838 <      
839 <      for(rb = mol->beginRigidBody(ri); rb != NULL;
840 <          rb = mol->nextRigidBody(ri)) {
841 <        rb->setGlobalIndex(beginRigidBodyIndex++);
704 <      }
705 <      
706 <      //local index of cutoff group is trivial, it only depends on the order of travesing
707 <      for(cg = mol->beginCutoffGroup(ci); cg != NULL;
708 <          cg = mol->nextCutoffGroup(ci)) {
709 <        cg->setGlobalIndex(beginCutoffGroupIndex++);
710 <      }
711 <    }
712 <    
838 > #endif          
839 >
840 >    } //end for(int i=0)  
841 >
842      //fill globalGroupMembership
843      std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
844      for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {        
# Line 721 | Line 850 | namespace OpenMD {
850          
851        }      
852      }
853 <    
853 >  
854   #ifdef IS_MPI    
855      // Since the globalGroupMembership has been zero filled and we've only
856      // poked values into the atoms we know, we can do an Allreduce
# Line 729 | Line 858 | namespace OpenMD {
858      // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
859      // docs said we could.
860      std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
861 <    MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
862 <                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
861 >    MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
862 >                              &tmpGroupMembership[0], nGlobalAtoms,
863 >                              MPI::INT, MPI::SUM);
864      info->setGlobalGroupMembership(tmpGroupMembership);
865   #else
866      info->setGlobalGroupMembership(globalGroupMembership);
# Line 747 | Line 877 | namespace OpenMD {
877      
878   #ifdef IS_MPI
879      std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
880 +    MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
881 +                              nGlobalAtoms,
882 +                              MPI::INT, MPI::SUM);
883      
751 –    MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
752 –                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
753 –    
884      info->setGlobalMolMembership(tmpMolMembership);
885   #else
886      info->setGlobalMolMembership(globalMolMembership);
# Line 766 | Line 896 | namespace OpenMD {
896      
897   #ifdef IS_MPI
898      std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
899 <    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
900 <                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
899 >    MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
900 >                              info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
901   #else
902      std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
903   #endif    
# Line 784 | Line 914 | namespace OpenMD {
914      for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
915        int myGlobalIndex = mol->getGlobalIndex();
916        int globalIO = startingIOIndexForMol[myGlobalIndex];
917 <      for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
918 <           integrableObject = mol->nextIntegrableObject(ioi)) {
919 <        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
920 <        IOIndexToIntegrableObject[globalIO] = integrableObject;
917 >      for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
918 >           sd = mol->nextIntegrableObject(ioi)) {
919 >        sd->setGlobalIntegrableObjectIndex(globalIO);
920 >        IOIndexToIntegrableObject[globalIO] = sd;
921          globalIO++;
922        }
923      }
924 <    
924 >      
925      info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
926      
927    }
928    
929    void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
930      Globals* simParams;
931 +
932      simParams = info->getSimParams();
933      
803 –    
934      DumpReader reader(info, mdFileName);
935      int nframes = reader.getNFrames();
936 <    
936 >
937      if (nframes > 0) {
938        reader.readFrame(nframes - 1);
939      } else {
# Line 814 | Line 944 | namespace OpenMD {
944        painCave.isFatal = 1;
945        simError();
946      }
817 –    
947      //copy the current snapshot to previous snapshot
948      info->getSnapshotManager()->advance();
949    }

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